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Shimizu K, Negishi L, Kurumizaka H, Suzuki M. Diversification of von Willebrand Factor A and Chitin-Binding Domains in Pif/BMSPs Among Mollusks. J Mol Evol 2024; 92:415-431. [PMID: 38864871 PMCID: PMC11291548 DOI: 10.1007/s00239-024-10180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/23/2024] [Indexed: 06/13/2024]
Abstract
Pif is a shell matrix protein (SMP) identified in the nacreous layer of Pinctada fucata (Pfu) comprised two proteins, Pif97 and Pif 80. Pif97 contains a von Willebrand factor A (VWA) and chitin-binding domains, whereas Pif80 can bind calcium carbonate crystals. The VWA domain is conserved in the SMPs of various mollusk species; however, their phylogenetic relationship remains obscure. Furthermore, although the VWA domain participates in protein-protein interactions, its role in shell formation has not been established. Accordingly, in the current study, we investigate the phylogenetic relationship between PfuPif and other VWA domain-containing proteins in major mollusk species. The shell-related proteins containing VWA domains formed a large clade (the Pif/BMSP family) and were classified into eight subfamilies with unique sequential features, expression patterns, and taxa diversity. Furthermore, a pull-down assay using recombinant proteins containing the VWA domain of PfuPif 97 revealed that the VWA domain interacts with five nacreous layer-related SMPs of P. fucata, including Pif 80 and nacrein. Collectively, these results suggest that the VWA domain is important in the formation of organic complexes and participates in shell mineralisation.
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Affiliation(s)
- Keisuke Shimizu
- Research Institute for Global Change, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-Cho, Yokosuka, Kanagawa, 237-0061, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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2
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Shikina S, Yoshioka Y, Chiu YL, Uchida T, Chen E, Cheng YC, Lin TC, Chu YL, Kanda M, Kawamitsu M, Fujie M, Takeuchi T, Zayasu Y, Satoh N, Shinzato C. Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp. Commun Biol 2024; 7:899. [PMID: 39048698 PMCID: PMC11269664 DOI: 10.1038/s42003-024-06544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.
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Affiliation(s)
- Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yi-Ling Chiu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Emma Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yin-Chu Cheng
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzu-Chieh Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Ling Chu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Miyuki Kanda
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.
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3
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Ricaurte M, Schizas NV, Weil EF, Ciborowski P, Boukli NM. Seasonal Proteome Variations in Orbicella faveolata Reveal Molecular Thermal Stress Adaptations. Proteomes 2024; 12:20. [PMID: 39051238 PMCID: PMC11270422 DOI: 10.3390/proteomes12030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Although seasonal water temperatures typically fluctuate by less than 4 °C across most tropical reefs, sustained heat stress with an increase of even 1 °C can alter and destabilize metabolic and physiological coral functions, leading to losses of coral reefs worldwide. The Caribbean region provides a natural experimental design to study how corals respond physiologically throughout the year. While characterized by warm temperatures and precipitation, there is a significant seasonal component with relative cooler and drier conditions during the months of January to February and warmer and wetter conditions during September and October. We conducted a comparative abundance of differentially expressed proteins with two contrasting temperatures during the cold and warm seasons of 2014 and 2015 in Orbicella faveolata, one of the most important and affected reef-building corals of the Caribbean. All presented proteoforms (42) were found to be significant in our proteomics differential expression analysis and classified based on their gene ontology. The results were accomplished by a combination of two-dimensional gel electrophoresis (2DE) to separate and visualize proteins and mass spectrometry (MS) for protein identification. To validate the differentially expressed proteins of Orbicella faveolata at the transcription level, qRT-PCR was performed. Our data indicated that a 3.1 °C increase in temperature in O. faveolata between the cold and warm seasons in San Cristobal and Enrique reefs of southwestern Puerto Rico was enough to affect the expression of a significant number of proteins associated with oxidative and heat stress responses, metabolism, immunity, and apoptosis. This research extends our knowledge into the mechanistic response of O. faveolata to mitigate thermal seasonal temperature variations in coral reefs.
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Affiliation(s)
- Martha Ricaurte
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, PR 00681, USA; (M.R.)
| | - Nikolaos V. Schizas
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, PR 00681, USA; (M.R.)
| | - Ernesto F. Weil
- Department of Marine Sciences, University of Puerto Rico, Mayagüez, Call Box 9000, Mayagüez, PR 00681, USA; (M.R.)
| | - Pawel Ciborowski
- Mass Spectrometry and Proteomics Core Facility, Durham Research Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nawal M. Boukli
- Biomedical Proteomics Facility, Microbiology and Immunology Department, Universidad Central del Caribe, Bayamón, PR 00960, USA
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Iguchi A, Gibu K, Yorifuji M, Nishijima M, Suzuki A, Ono T, Matsumoto Y, Inoue M, Fujii M, Muraoka D, Fujita Y, Takami H. Transgenerational acclimation to acidified seawater and gene expression patterns in a sea urchin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172616. [PMID: 38642751 DOI: 10.1016/j.scitotenv.2024.172616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
Transgenerational responses of susceptible calcifying organisms to progressive ocean acidification are an important issue in reducing uncertainty of future predictions. In this study, a two-generation rearing experiment was conducted using mature Mesocentrotus nudus, a major edible sea urchin that occurs along the coasts of northern Japan. Morphological observations and comprehensive gene expression analysis (RNA-seq) of resulting larvae were performed to examine transgenerational acclimation to acidified seawater. Two generations of rearing experiments showed that larvae derived from parents acclimated to acidified seawater tended to have higher survival and show less reduction in body size when exposed to acidified seawater of the same pH, suggesting that a positive carry-over effect occurred. RNA-seq analysis showed that gene expression patterns of larvae originated from both acclimated and non-acclimated parents to acidified seawater tended to be different than control condition, and the gene expression pattern of larvae originated from acclimated parents was substantially different than that of larvae of non-acclimated and control parents.
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Affiliation(s)
- Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan; Research laboratory on environmentally-conscious developments and technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan.
| | - Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Makiko Yorifuji
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Miyuki Nishijima
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan; Research laboratory on environmentally-conscious developments and technologies [E-code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8567, Japan
| | - Tsuneo Ono
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Yokohama 236-8648, Japan
| | - Yukio Matsumoto
- Japan Fisheries Research and Education Agency, Fisheries Technology Institute, Miyako Laboratory, Miyako 027-0097, Japan
| | - Mayuri Inoue
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Masahiko Fujii
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo 060-810, Japan
| | - Daisuke Muraoka
- Japan Fisheries Research and Education Agency, Fisheries Technology Institute, Miyako Laboratory, Miyako 027-0097, Japan
| | - Yamato Fujita
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-810, Japan
| | - Hideki Takami
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Shiogama Laboratory, 3-27-5, Shiogama 985-0001, Japan
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Radice VZ, Martinez A, Paytan A, Potts DC, Barshis DJ. Complex dynamics of coral gene expression responses to low pH across species. Mol Ecol 2024; 33:e17186. [PMID: 37905582 DOI: 10.1111/mec.17186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/25/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges ('Ojo'; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2-year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef-building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef). Transplant pH environment had the greatest effect on gene expression of Porites astreoides hosts and symbionts and P. porites hosts. Host P. astreoides Ojo natives transplanted to ambient pH showed a similar gene expression profile to Lagoon natives remaining in ambient pH, providing evidence of plasticity in response to ambient pH conditions. Although origin had a larger effect on host S. siderea gene expression due to differences in symbiont genera within Reef and Lagoon/Ojo natives, subtle effects of low pH on all origins demonstrated acclimatization potential. All corals responded to low pH by differentially expressing genes related to pH regulation, ion transport, calcification, cell adhesion and stress/immune response. This study demonstrates that the magnitude of coral gene expression responses to pH varies considerably among populations, species and holobionts, which could differentially affect acclimatization to and impacts of ocean acidification.
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Affiliation(s)
- Veronica Z Radice
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
| | - Ana Martinez
- University of California, Santa Cruz, California, USA
| | - Adina Paytan
- University of California, Santa Cruz, California, USA
| | | | - Daniel J Barshis
- Department of Biological Sciences, Old Dominion University, Norfolk, Virginia, USA
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Rico-Esenaro SD, de Jesús Adolfo Tortolero-Langarica J, Iglesias-Prieto R, Carricart-Ganivet JP. The δ 15N in Orbicella faveolata organic matter reveals anthropogenic impact by sewage inputs in a Mexican Caribbean coral reef lagoon. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:118872-118880. [PMID: 37919495 DOI: 10.1007/s11356-023-30476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Coral-reef ecosystems provide essentials services to human societies, representing the most important source of income (e.g., tourism and artisanal fishing) for many coastal developing countries. In the Caribbean region, most touristic and coastal developments are in the vicinity of coral reefs where they may contribute to reef degradation. Here we evaluated the influence of sewage inputs in the coral reef lagoon of Puerto Morelos during a period of 40 years (1970-2012). Annual δ15N values were determined in the organic matter (OM) extracted from coral skeletons of Orbicella faveolata. Average protein content in the OM was 0.33 mg of protein g-1 CaCO3 (±0.10 SD) and a 0.03% of OM relative to the sample weight (n =100). The average of N g-1 CaCO3 was 0.002% (± 0.001 SD). The results showed an increase (p < 0.001) in δ15N over the time, positively correlated with population growth derived from touristic development. These findings emphasize the need to generate urban-planning remediation strategies that consider the impact on natural environments, reduce sewage pollution, and mitigate local stressors that threaten the status of coral-reef communities in the Caribbean region.
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Affiliation(s)
- Serguei Damián Rico-Esenaro
- Laboratorio de Esclerocronología de Corales Arrecifales, Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Prol. Av. Niños Héroes S/N, Domicilio conocido, Puerto Morelos, Q. Roo, 77580, México
- Departamento El Hombre y su Ambiente, Universidad Autónoma Metropolitana Unidad Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacán, Cd. de México, 04960, México
| | - José de Jesús Adolfo Tortolero-Langarica
- Laboratorio de Esclerocronología de Corales Arrecifales, Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Prol. Av. Niños Héroes S/N, Domicilio conocido, Puerto Morelos, Q. Roo, 77580, México
- Tecnológico Nacional de México/IT Bahía de Banderas, Crucero a Punta de Mita S/N, Bahía de Banderas, 63734, Nayarit, México
| | - Roberto Iglesias-Prieto
- Department of Biology, The Pennsylvania State University, 208 Mueller Lab, University Park, PA, 16802, USA
| | - Juan P Carricart-Ganivet
- Laboratorio de Esclerocronología de Corales Arrecifales, Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Prol. Av. Niños Héroes S/N, Domicilio conocido, Puerto Morelos, Q. Roo, 77580, México.
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7
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Han T, Liao X, Guo Z, Chen JY, He C, Lu Z. Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade. Front Genet 2023; 14:1297483. [PMID: 38028626 PMCID: PMC10662330 DOI: 10.3389/fgene.2023.1297483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.
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Affiliation(s)
- Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Zhuojun Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - J.-Y. Chen
- Nanjing Institute of Geology and Paleontology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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8
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Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
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Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire Des Sciences du Climat Et de L'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
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9
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Binet MT, Reichelt-Brushett A, McKnight K, Golding LA, Humphrey C, Stauber JL. Adult Corals Are Uniquely More Sensitive to Manganese Than Coral Early-Life Stages. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1359-1370. [PMID: 36946339 DOI: 10.1002/etc.5618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/08/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
Manganese (Mn) is an essential element and is generally considered to be one of the least toxic metals to aquatic organisms, with chronic effects rarely seen at concentrations below 1000 µg/L. Anthropogenic activities lead to elevated concentrations of Mn in tropical marine waters. Limited data suggest that Mn is more acutely toxic to adults than to early life stages of scleractinian corals in static renewal tests. However, to enable the inclusion of sufficient sensitive coral data in species sensitivity distributions to derive water quality guideline values for Mn, we determined the acute toxicity of Mn to the adult scleractinian coral, Acropora muricata, in flow-through exposures. The 48-h median effective concentration was 824 µg Mn/L (based on time-weighted average, measured, dissolved Mn). The endpoint was tissue sloughing, a lethal process by which coral tissue detaches from the coral skeleton. Tissue sloughing was unrelated to superoxidase dismutase activity in coral tissue, and occurred in the absence of bleaching, that is, toxic effects were observed for the coral host, but not for algal symbionts. We confirm that adult scleractinian corals are uniquely sensitive to Mn in acute exposures at concentrations 10-340 times lower than those reported to cause acute or chronic toxicity to coral early life stages, challenging the traditional notion that early life stages are more sensitive than mature organisms. Environ Toxicol Chem 2023;00:1-12. © 2023 Commonwealth Scientific and Industrial Research Organisation. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Monique T Binet
- Centre for Environmental Contaminants Research, Commonwealth Scientific and Industial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
| | - Amanda Reichelt-Brushett
- School of Environment, Science and Engineering, Southern Cross University, Lismore, New South Wales, Australia
| | - Kitty McKnight
- The National Sea Simulator, Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Lisa A Golding
- Centre for Environmental Contaminants Research, Commonwealth Scientific and Industial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
| | - Craig Humphrey
- The National Sea Simulator, Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Jenny L Stauber
- Centre for Environmental Contaminants Research, Commonwealth Scientific and Industial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
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10
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Different skeletal protein toolkits achieve similar structure and performance in the tropical coral Stylophora pistillata and the temperate Oculina patagonica. Sci Rep 2022; 12:16575. [PMID: 36195656 PMCID: PMC9532382 DOI: 10.1038/s41598-022-20744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/19/2022] [Indexed: 11/08/2022] Open
Abstract
Stony corals (order: Scleractinia) differ in growth form and structure. While stony corals have gained the ability to form their aragonite skeleton once in their evolution, the suite of proteins involved in skeletogenesis is different for different coral species. This led to the conclusion that the organic portion of their skeleton can undergo rapid evolutionary changes by independently evolving new biomineralization-related proteins. Here, we used liquid chromatography-tandem mass spectrometry to sequence skeletogenic proteins extracted from the encrusting temperate coral Oculina patagonica. We compare it to the previously published skeletal proteome of the branching subtropical corals Stylophora pistillata as both are regarded as highly resilient to environmental changes. We further characterized the skeletal organic matrix (OM) composition of both taxa and tested their effects on the mineral formation using a series of overgrowth experiments on calcite seeds. We found that each species utilizes a different set of proteins containing different amino acid compositions and achieve a different morphology modification capacity on calcite overgrowth. Our results further support the hypothesis that the different coral taxa utilize a species-specific protein set comprised of independent gene co-option to construct their own unique organic matrix framework. While the protein set differs between species, the specific predicted roles of the whole set appear to underline similar functional roles. They include assisting in forming the extracellular matrix, nucleation of the mineral and cell signaling. Nevertheless, the different composition might be the reason for the varying organization of the mineral growth in the presence of a particular skeletal OM, ultimately forming their distinct morphologies.
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11
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Shimizu K, Takeuchi T, Negishi L, Kurumizaka H, Kuriyama I, Endo K, Suzuki M. Evolution of EGF-like and Zona pellucida domains containing shell matrix proteins in mollusks. Mol Biol Evol 2022; 39:6633355. [PMID: 35796746 PMCID: PMC9290575 DOI: 10.1093/molbev/msac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several types of shell matrix proteins (SMPs) have been identified in molluskan shells. Their diversity is the consequence of various molecular processes, including domain shuffling and gene duplication. However, the evolutionary origin of most SMPs remains unclear. In this study, we investigated the evolutionary process EGF-like and zona pellucida (ZP) domains containing SMPs. Two types of the proteins (EGF-like protein (EGFL) and EGF-like and ZP domains containing protein (EGFZP)) were found in the pearl oyster, Pinctada fucata. In contrast, only EGFZP was identified in the gastropods. Phylogenetic analysis and genomic arrangement studies showed that EGFL and EGFZP formed a clade in bivalves, and their encoding genes were localized in tandem repeats on the same scaffold. In P. fucata, EGFL genes were expressed in the outer part of mantle epithelial cells are related to the calcitic shell formation. However, in both P. fucata and the limpet Nipponacmea fuscoviridis, EGFZP genes were expressed in the inner part of the mantle epithelial cells are related to aragonitic shell formation. Furthermore, our analysis showed that in P. fucata, the ZP domain interacts with eight SMPs that have various functions in the nacreous shell mineralization. The data suggest that the ZP domain can interact with other SMPs, and EGFL evolution in pterimorph bivalves represents an example of neo-functionalization that involves the acquisition of a novel protein through gene duplication.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, 3564-3 Hamajima, Hamajima-cho, Shima-city, Mie 517-0404, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
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12
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Seiblitz IGL, Vaga CF, Capel KCC, Cairns SD, Stolarski J, Quattrini AM, Kitahara MV. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol Phylogenet Evol 2022; 175:107565. [PMID: 35787457 DOI: 10.1016/j.ympev.2022.107565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 10/17/2022]
Abstract
Molecularly, the family Caryophylliidae is polyphyletic and different sets of genetic data converge towards a consensus that a taxonomic review of this family is necessary. Overall, the order of genes in the mitochondrial genome (mitogenome) together with DNA sequences have been used to successfully untangle evolutionary relationships in several groups of organisms. Published mitogenomes of two caryophylliid genera (Desmophyllum and Solenosmilia) present a transposition of the gene block containing cob, nad2, and nad6, which is located between nad5 5' exon and trnW, while that of Polycyathus chaishanensis presents the same gene order as the majority of scleractinian corals. In molecular-based evolutionary reconstructions, caryophylliids that have the mitochondrial gene rearrangement were recovered as a monophyletic lineage ("true" caryophylliids), while members of the genus Polycyathus were placed in a different position. In this study, additional mitogenomes of this family were assembled and included in evolutionary reconstructions of Scleractinia in order to improve our understanding on whether the mitogenome gene rearrangement is limited to and, therefore, could be a synapomorphy of the actual members of Caryophylliidae. Specimens of Caryophyllia scobinosa, Premocyathus sp., Heterocyathus sulcatus, and Trochocyathus caryophylloides, as well as Desmophyllum pertusum and Solenosmilia variabilis from the Southwest Atlantic were sequenced using Illumina platforms. Then, mitochondrial genomes were assembled and annotated, and nuclear datasets were recovered in-silico from assembled contigs using a previously published set of baits. Evolutionary reconstructions were performed using mitochondrial and nuclear datasets and based on Maximum Likelihood and Bayesian Inference. Obtained mitogenomes are circular and range between 15,816 and 18,225 bp in size and from 30.76% to 36.63% in GC content. The gene rearrangement is only seen in C. scobinosa, D. pertusum, Premocyathus sp., and S. variabilis, which were recovered as a monophyletic clade in both mitochondrial and nuclear phylogenies. On the other hand, the "caryophylliids" with the canonical mitogenome gene order were not recovered within this clade. Differences in features of the skeleton of "true" caryophylliids in comparison to traditional members of the family were observed and offer further support that the gene rearrangement might be seen as a synapomorphy of family Caryophylliidae.
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Affiliation(s)
- I G L Seiblitz
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil.
| | - C F Vaga
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - K C C Capel
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, PL-00-818 Warsaw, Poland
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163 United States of America
| | - M V Kitahara
- Centre for Marine Biology, University of São Paulo, 11612-109 São Sebastião, Brazil; Department of Marine Science, Federal University of São Paulo, 11070-100 Santos, Brazil.
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13
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Gibu K, Ikeuchi E, Bell T, Nakamura T, Yoshioka Y, Suzuki A, Iguchi A. Calcification rates of a massive and a branching coral species were unrelated to diversity of endosymbiotic dinoflagellates. Mol Biol Rep 2022; 49:9101-9106. [PMID: 35737176 DOI: 10.1007/s11033-022-07702-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/10/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND To explore the possibility that endosymbiotic dinoflagellates (Symbiodiniaceae) are associated with coral calcification rates, we investigated the diversity of symbiotic algae in coral colonies with different calcification rates within massive and branching corals (Porites australiensis and Acropora digitifera). METHODS AND RESULTS Genotyping symbiotic algae from colonies with different calcification rates revealed that all the colonies of both species harbored mainly Cladocopium (previously clade C of Symbiodinium). The Cladocopium symbionts in P. australiensis were mainly composed of C15 and C15bn, and those in A. digitifera of C50a and C50c. We did not detect clear relationships between symbiont compositions and calcification rates within the two coral species. CONCLUSIONS Our results suggest that different coral calcification rates within species may be attributed to genetic factors of coral hosts themselves and/or within symbiont genotypes.
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Affiliation(s)
- Kodai Gibu
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Eri Ikeuchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Tomoko Bell
- Water and Environmental Research Institute, University of Guam, UOG Station, Mangilao, GU, 96923, USA
| | - Takashi Nakamura
- Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa, 905-2192, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.,Research Laboratory On Environmentally-Conscious Developments and Technologies [E-Code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan. .,Research Laboratory On Environmentally-Conscious Developments and Technologies [E-Code], National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan.
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14
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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15
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Haridi A. Identification, diversity and domain structure analysis of mucin and mucin-like genes in sea anemone Actinia tenebrosa. PeerJ 2022; 10:e13292. [PMID: 35539013 PMCID: PMC9080433 DOI: 10.7717/peerj.13292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Mucins are part of the glycoprotein family and the main proteinaceous component of mucus. The sea anemone species, Actinia tenebrosa (Phylum Cnidaria) produce large amounts of mucus, which have not been studied in detail. Furthermore, there has only been limited investigation of mucin genes in phylum Cnidaria. Therefore, the aim of current study was to identify and analyse the repertoire mucin genes present in A. tenebrosa and range of other sea anemone species to document their diversity in this group. Methods To achieve this aim, we undertook transcriptome sequencing, assembly, and annotation to identify mucin genes in A. tenebrosa. Results The results from this study demonstrated a diverse repertoire of mucin proteins, including mucin1-like, mucin4-like, and a range of mucin-like genes in the range of sea anemone species examined. The domain structure of the identified mucin genes was found to be consistent with the conserved domains found in the homologous proteins of vertebrate species. The discovery of a diverse range of mucin genes in sea anemone species provided a basic reference for future mucin studies in cnidarians and could lead to research into their application in the pharmacological, clinical, and cosmetic industries.
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16
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Levy S, Mass T. The Skeleton and Biomineralization Mechanism as Part of the Innate Immune System of Stony Corals. Front Immunol 2022; 13:850338. [PMID: 35281045 PMCID: PMC8913943 DOI: 10.3389/fimmu.2022.850338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022] Open
Abstract
Stony corals are among the most important calcifiers in the marine ecosystem as they form the coral reefs. Coral reefs have huge ecological importance as they constitute the most diverse marine ecosystem, providing a home to roughly a quarter of all marine species. In recent years, many studies have shed light on the mechanisms underlying the biomineralization processes in corals, as characterizing the calicoblast cell layer and genes involved in the formation of the calcium carbonate skeleton. In addition, considerable advancements have been made in the research field of coral immunity as characterizing genes involved in the immune response to pathogens and stressors, and the revealing of specialized immune cells, including their gene expression profile and phagocytosis capabilities. Yet, these two fields of corals research have never been integrated. Here, we discuss how the coral skeleton plays a role as the first line of defense. We integrate the knowledge from both fields and highlight genes and proteins that are related to biomineralization and might be involved in the innate immune response and help the coral deal with pathogens that penetrate its skeleton. In many organisms, the immune system has been tied to calcification. In humans, immune factors enhance ectopic calcification which causes severe diseases. Further investigation of coral immune genes which are involved in skeleton defense as well as in biomineralization might shed light on our understanding of the correlation and the interaction of both processes as well as reveal novel comprehension of how immune factors enhance calcification.
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Affiliation(s)
- Shani Levy
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
- *Correspondence: Shani Levy, ; Tali Mass,
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
- *Correspondence: Shani Levy, ; Tali Mass,
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17
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Shinzato C, Takeuchi T, Yoshioka Y, Tada I, Kanda M, Broussard C, Iguchi A, Kusakabe M, Marin F, Satoh N, Inoue M. Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918. Genome Biol Evol 2021; 13:6456307. [PMID: 34878117 PMCID: PMC8691061 DOI: 10.1093/gbe/evab270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes. Proteome analysis identified 60 Porites skeletal matrix protein genes, all of which show significant similarities to genes from other corals and even to those from a sea anemone, which has no skeleton. Nonetheless, 30% of its skeletal matrix proteins were unique to Porites and were not present in the skeletons of other corals. Comparative genomic analyses showed that genes widely conserved among other organisms are selectively expanded in Porites. Specifically, comparisons of transcriptomic responses of P. australiensis and Acropora digitifera, a stress-sensitive coral, reveal significant differences in regard to genes that respond to increased water temperature, and some of the genes expanded exclusively in Porites may account for the different thermal tolerances of these corals. Taken together, widely shared genes may have given rise to unique biological characteristics of Porites, massive skeletons and stress tolerance.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | | | - Frédéric Marin
- Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne, Dijon, France
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayuri Inoue
- Division of Earth Science, Graduate School of Natural Science and Technology, Okayama University, Japan
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18
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Wang X, Zoccola D, Liew YJ, Tambutte E, Cui G, Allemand D, Tambutte S, Aranda M. The Evolution of Calcification in Reef-Building Corals. Mol Biol Evol 2021; 38:3543-3555. [PMID: 33871620 PMCID: PMC8382919 DOI: 10.1093/molbev/msab103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.
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Affiliation(s)
- Xin Wang
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Didier Zoccola
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Yi Jin Liew
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Eric Tambutte
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Guoxin Cui
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | - Denis Allemand
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Sylvie Tambutte
- Marine Biology Department, Centre Scientifique de Monaco, Monaco, Monaco
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
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19
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Habuddha V, Suwannasing C, Buddawong A, Seenprachawong K, Duangchan T, Sombutkayasith C, Supokawej A, Weerachatyanukul W, Asuvapongpatana S. Characterization of Thrombospondin Type 1 Repeat in Haliotis diversicolor and Its Possible Role in Osteoinduction. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:641-652. [PMID: 34471969 DOI: 10.1007/s10126-021-10054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Thrombospondin repeats (TSR) are important peptide domains present in the sequences of many extracellular and transmembrane proteins with which a variety of ligands interact. In this study, we characterized HdTSR domains in the ADAMTS3 protein of Thai abalone, Haliotis diversicolor, based on the transcriptomic analysis of its mantle tissues. PCR amplification and localization studies demonstrated the existence of HdTSR transcript and protein in H. diversicolor tissues, particularly in both the inner and outer mantle epithelial folds. We, therefore, generated a short recombinant protein, termed HdTSR1/2, based on the existence of the WxxWxxW or WxxxxW motif (which binds to TGF-β, a known signaling in bone formation/repair) in HdTSR1 and HdTSR2 sequences and used it to test the osteoinduction function in the pre-osteoblastic cell line, MC3T3-E1. This recombinant protein demonstrated the ability to induce the differentiation of MC3T3-E1 cells by the concentration- and time-dependent upregulation of many known osteogenic markers, including RUNX2, COL1A1, OCN, and OPN. We also demonstrated the upregulation of the SMAD2 gene after cell treatment with HdTSR1/2 proteinindicating its possible interaction through TGF-β, which thus activates its downstream signaling cascade and triggers the biomineralization process in the differentiated osteoblastic cells. Together, HdTSR domains existed in an extracellular ADAMTS3 protein in the mantle epithelium of H. diversicolor and played a role in osteoinduction as similar to the other nacreous proteins, opening up its possibility to be developed as an inducing agent of bone repair.
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Affiliation(s)
- Valainipha Habuddha
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
- School of Allied Health Science, Walailak University, Nakhon Si Thammarat, Thailand
| | - Chanyatip Suwannasing
- Department of Radiological Technology, Faculty of Allied Health Sciences, Naresuan University, Phitsanulok, Thailand
| | - Aticha Buddawong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
- Chulabhorn International College of Medicine, Thammasat University, Khlong Nueng Pathumthani 12121, Rangsit Campus, Thailand
| | - Kanokwan Seenprachawong
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University (Salaya Campus), Salaya, Nakhonpathom, Thailand
| | - Thitinat Duangchan
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University (Salaya Campus), Salaya, Nakhonpathom, Thailand
| | | | - Aungkura Supokawej
- Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University (Salaya Campus), Salaya, Nakhonpathom, Thailand
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20
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Conci N, Lehmann M, Vargas S, Wörheide G. Comparative Proteomics of Octocoral and Scleractinian Skeletomes and the Evolution of Coral Calcification. Genome Biol Evol 2021; 12:1623-1635. [PMID: 32761183 PMCID: PMC7533068 DOI: 10.1093/gbe/evaa162] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2020] [Indexed: 12/23/2022] Open
Abstract
Corals are the ecosystem engineers of coral reefs, one of the most biodiverse marine ecosystems. The ability of corals to form reefs depends on the precipitation of calcium carbonate (CaCO3) under biological control. However, several mechanisms underlying coral biomineralization remain elusive, for example, whether corals employ different molecular machineries to deposit different CaCO3 polymorphs (i.e., aragonite or calcite). Here, we used tandem mass spectrometry (MS/MS) to compare the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata (calcite sclerites), the blue coral Heliopora coerulea (aragonitic skeleton), and the scleractinian aragonitic Montipora digitata. Reciprocal Blast analysis revealed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites. However, the carbonic anhydrase CruCA4 is present in the skeletons of both polymorphs. Phylogenetic analysis highlighted several possible instances of protein co-option in octocorals. These include acidic proteins and scleritin, which appear to have been secondarily recruited for calcification and likely derive from proteins playing different functions. Similarities between octocorals and scleractinians included presence of a galaxin-related protein, carbonic anhydrases, and one hephaestin-like protein. Although the first two appear to have been independently recruited, the third appear to share a common origin. This work represents the first attempt to identify and compare proteins associated with coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of coral biomineralization.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Martin Lehmann
- Department of Biology I-Botany, Biozentrum der LMU München, Planegg-Martinsried, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany.,GeoBio-Center LMU, Ludwig-Maximilians-Universität München, München, Germany
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21
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Shinzato C, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N. Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes. Mol Biol Evol 2021; 38:16-30. [PMID: 32877528 PMCID: PMC7783167 DOI: 10.1093/molbev/msaa216] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Miyuki Kanda
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Go Suzuki
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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22
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Mummadisetti MP, Drake JL, Falkowski PG. The spatial network of skeletal proteins in a stony coral. J R Soc Interface 2021; 18:20200859. [PMID: 33622149 PMCID: PMC8086859 DOI: 10.1098/rsif.2020.0859] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coral skeletons are materials composed of inorganic aragonitic fibres and organic molecules including proteins, sugars and lipids that are highly organized to form a solid biomaterial upon which the animals live. The skeleton contains tens of proteins, all of which are encoded in the animal genome and secreted during the biomineralization process. While recent advances are revealing the functions and evolutionary history of some of these proteins, how they are spatially arranged in the skeleton is unknown. Using a combination of chemical cross-linking and high-resolution tandem mass spectrometry, we identify, for the first time, the spatial interactions of the proteins embedded within the skeleton of the stony coral Stylophora pistillata. Our subsequent network analysis revealed that several coral acid-rich proteins are invariably associated with carbonic anhydrase(s), alpha-collagen, cadherins and other calcium-binding proteins. These spatial arrangements clearly show that protein-protein interactions in coral skeletons are highly coordinated and are key to understanding the formation and persistence of coral skeletons through time.
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Affiliation(s)
- Manjula P Mummadisetti
- Environmental Biophysics and Molecular Biology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Rd, New Brunswick, NJ 08901, USA
| | - Jeana L Drake
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, 595 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,Department of Marine Biology, University of Haifa, 199 Aba Khoushy Avenue, Mount Carmel, Haifa 2498838, Israel
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Biology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Rd, New Brunswick, NJ 08901, USA.,Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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23
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Zaquin T, Malik A, Drake JL, Putnam HM, Mass T. Evolution of Protein-Mediated Biomineralization in Scleractinian Corals. Front Genet 2021; 12:618517. [PMID: 33633782 PMCID: PMC7902050 DOI: 10.3389/fgene.2021.618517] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene.
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Affiliation(s)
- Tal Zaquin
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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24
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Molecular and skeletal fingerprints of scleractinian coral biomineralization: From the sea surface to mesophotic depths. Acta Biomater 2021; 120:263-276. [PMID: 31954936 DOI: 10.1016/j.actbio.2020.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 11/20/2022]
Abstract
Reef-building corals, the major producers of biogenic calcium carbonate, form skeletons in a plethora of morphological forms. Here we studied skeletal modifications of Stylophora pistillata (clade 4) colonies that adapt to increasing depths with decreasing ambient light. The coral show characteristic transitions from spherical morphologies (shallow depths, 5 m deep) to flat and branching geometries (mesophotic depths, 60 m deep). Such changes are typically ascribed to the algal photosymbiont physiological feedback with the coral that host them. We find specific fine-scale skeletal variability in accretion of structure at shallow- and mesophotic depth morphotypes that suggest underlying genomic regulation of biomineralization pathways of the coral host. To explain this, we conducted comparative morphology-based analyses, including optical and electron microscopy, tomography and X-ray diffraction analysis coupled with a comprehensive transcriptomic analysis of S. pistillata. The samples originated from Gulf of Eilat in the Red Sea collected along a depth gradient from shallow to mesophotic depths (5 to 60 m). Additional samples were experimentally transplanted from 5 m to 60 m and from 60 m to 5 m. Interestingly, both morphologically and functionally, transplanted corals partly adapt by exhibiting typical depth-specific properties. In mesophotic depths, we find that the organic matrix fraction is enriched in the coralla, well matching the overrepresentation of transcripts encoding biomineralization "tool-kit" structural extracellularproteins that was observed. These results provide insights into the molecular mechanisms of calcification and skeletal adaptation that repeatedly allowed this coral group to adapt to a range of environments presumably with a rich geological past. STATEMENT OF SIGNIFICANCE: Understanding the reef coral physiological plasticity under a rapidly changing climate is of crucial importance for the protection of coral reef ecosystems. Most of the reef corals operate near their upper limit of heat tolerance. A possible rescue for some coral species is migration to deeper, cooler mesophotic depths. However, gradually changing environmental parameters (especially light) along the depth gradient pose new adaptative stress on corals with largely unknown influences on the various biological molecular pathways. This work provides a first comprehensive analysis of changes in gene expression, including biomineralization "tool kit" genes, and reports the fine-scale microstructural and crystallographic skeletal details in S. pistillata collected in the Red Sea along a depth gradient spannign 5 to 60 m.
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25
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Le Roy N, Ganot P, Aranda M, Allemand D, Tambutté S. The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals. BMC Ecol Evol 2021; 21:1. [PMID: 33514311 PMCID: PMC7853314 DOI: 10.1186/s12862-020-01734-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/13/2020] [Indexed: 12/16/2022] Open
Abstract
Background The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals. Results We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution. Conclusion Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.
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Affiliation(s)
- Nathalie Le Roy
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco. .,BOA UMR83, INRAe Centre Val de Loire, 37380, Nouzilly, France.
| | - Philippe Ganot
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
| | - Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, 8 Quai Antoine 1er, Monaco, MC, 98000, Monaco
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26
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Shimizu K, Kintsu H, Awaji M, Matumoto T, Suzuki M. Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata. J Mol Evol 2020; 88:742-758. [PMID: 33236260 DOI: 10.1007/s00239-020-09977-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructures, the nacreous and prismatic layers. Nacreous and prismatic layer-specific matrix proteins have been reported in Pteriidae bivalves, but remain unclear in Pinnidae. We performed transcriptome analysis using the mantle cells of A. pectinata to screen the candidate transcripts involved in its prismatic layer formation. We found Asprich and nine highly conserved prismatic layer-specific SMPs encoding transcript in P. fucata, P. margaritifera, and P. maxima (Tyrosinase, Chitinase, EGF-like proteins, Fibronectin, valine-rich proteins, and prismatic uncharacterized shell protein 2 [PUSP2]) using molecular phylogenetic analysis or multiple alignment. We confirmed these genes were expressed in the epithelial cells of the mantle edge (outer surface of the outer fold) and the mantle pallium. Phylogenetic character mapping of these SMPs was used to infer a possible evolutionary scenario of them in Pteriomorphia. EGF-like proteins, Fibronectin, and valine-rich proteins encoding genes each evolved in the linage leading to four Pteriomorphia (Mytilidae, Pinnidae, Ostreidae, and Pteriidae), PUSP2 evolved in the linage leading to three Pteriomorphia families (Pinnidae, Ostreidae, and Pteriidae), and chitinase was independently evolved as SMPs in Mytilidae and in other Pteriomorphia (Pinnidae, Ostreidae, and Pteriidae). Our results provide a new dataset for A. pectinata SMP annotation, and a basis for understanding the evolution of prismatic layer formation in bivalves.
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Affiliation(s)
- Keisuke Shimizu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyuki Kintsu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.,Center for Health and Environmental Risk Research, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masahiko Awaji
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Toshie Matumoto
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 422-1 Nakatsuhama, Minami-Ise, Watarai, Mie, 516-0193, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan.
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27
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Drake JL, Whitelegge JP, Jacobs DK. First sequencing of ancient coral skeletal proteins. Sci Rep 2020; 10:19407. [PMID: 33173075 PMCID: PMC7655939 DOI: 10.1038/s41598-020-75846-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Here we report the first recovery, sequencing, and identification of fossil biomineral proteins from a Pleistocene fossil invertebrate, the stony coral Orbicella annularis. This fossil retains total hydrolysable amino acids of a roughly similar composition to extracts from modern O. annularis skeletons, with the amino acid data rich in Asx (Asp + Asn) and Glx (Glu + Gln) typical of invertebrate skeletal proteins. It also retains several proteins, including a highly acidic protein, also known from modern coral skeletal proteomes that we sequenced by LC-MS/MS over multiple trials in the best-preserved fossil coral specimen. A combination of degradation or amino acid racemization inhibition of trypsin digestion appears to limit greater recovery. Nevertheless, our workflow determines optimal samples for effective sequencing of fossil coral proteins, allowing comparison of modern and fossil invertebrate protein sequences, and will likely lead to further improvements of the methods. Sequencing of endogenous organic molecules in fossil invertebrate biominerals provides an ancient record of composition, potentially clarifying evolutionary changes and biotic responses to paleoenvironments.
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Affiliation(s)
- Jeana L Drake
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
- Department of Marine Biology, University of Haifa, Haifa, Israel.
| | | | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA.
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, USA.
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28
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Cooke I, Ying H, Forêt S, Bongaerts P, Strugnell JM, Simakov O, Zhang J, Field MA, Rodriguez-Lanetty M, Bell SC, Bourne DG, van Oppen MJ, Ragan MA, Miller DJ. Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts. SCIENCE ADVANCES 2020; 6:6/48/eabc6318. [PMID: 33246955 PMCID: PMC7695477 DOI: 10.1126/sciadv.abc6318] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/15/2020] [Indexed: 05/24/2023]
Abstract
Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.
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Affiliation(s)
- Ira Cooke
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Pim Bongaerts
- California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Jia Zhang
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Mauricio Rodriguez-Lanetty
- Institute of Environment and Department of Biological Sciences, Florida International University, Miami, Fl 33199, USA
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - David G Bourne
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Madeleine Jh van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of BioSciences, University of Melbourne, Melbourne, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
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Chiu YL, Shikina S, Yoshioka Y, Shinzato C, Chang CF. De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. BMC Genomics 2020; 21:732. [PMID: 33087060 PMCID: PMC7579821 DOI: 10.1186/s12864-020-07113-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesis, we isolated ovaries and testes at different developmental phases from a gonochoric coral, Euphyllia ancora, and adopted a transcriptomic approach to reveal sex- and phase-specific gene expression profiles. In particular, we explored genes associated with oocyte development and maturation, spermiogenesis, sperm motility / capacitation, and fertilization. RESULTS 1.6 billion raw reads were obtained from 24 gonadal samples. De novo assembly of trimmed reads, and elimination of contigs derived from symbiotic dinoflagellates (Symbiodiniaceae) and other organisms yielded a reference E. ancora gonadal transcriptome of 35,802 contigs. Analysis of 4 developmental phases identified 2023 genes that were differentially expressed during oogenesis and 678 during spermatogenesis. In premature/mature ovaries, 631 genes were specifically upregulated, with 538 in mature testes. Upregulated genes included those involved in gametogenesis, gamete maturation, sperm motility / capacitation, and fertilization in other metazoans, including humans. Meanwhile, a large number of genes without homology to sequences in the SWISS-PROT database were also observed among upregulated genes in premature / mature ovaries and mature testes. CONCLUSIONS Our findings show that scleractinian gametogenesis shares many molecular characteristics with that of other metazoans, but it also possesses unique characteristics developed during cnidarian and/or scleractinian evolution. To the best of our knowledge, this study is the first to create a gonadal transcriptome assembly from any scleractinian. This study and associated datasets provide a foundation for future studies regarding gametogenesis and differences between male and female colonies from molecular and cellular perspectives. Furthermore, our transcriptome assembly will be a useful reference for future development of sex-specific and/or stage-specific germ cell markers that can be used in coral aquaculture and ecological studies.
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Affiliation(s)
- Yi-Ling Chiu
- Doctoral Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan.,Doctoral Program in Marine Biotechnology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan. .,Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
| | - Ching-Fong Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan. .,Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.
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30
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Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers. Sci Rep 2020; 10:15432. [PMID: 32963271 PMCID: PMC7508986 DOI: 10.1038/s41598-020-72112-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/17/2020] [Indexed: 11/25/2022] Open
Abstract
Coral reef habitats surrounding Cuba include relatively healthy, well-developed shallow and mesophotic (30–150 m) scleractinian communities at the cross-currents of the Tropical Western Atlantic (TWA). However, Cuba’s coral communities are not immune to the declines observed throughout the TWA, and there is limited information available regarding genetic connectivity, diversity, and structure among these populations. This represents an immense gap in our understanding of coral ecology and population dynamics at both local and regional scales. To address this gap, we evaluated the population genetic structure of the coral Montastraea cavernosa across eight reef sites surrounding Cuba. Colonies were genotyped using nine microsatellite markers and > 9,000 single nucleotide polymorphism (SNP) markers generated using the 2bRAD approach to assess fine-scale genetic structure across these sites. Both the microsatellite and SNP analyses identified patterns of genetic differentiation among sample populations. While the microsatellite analyses did not identify significant genetic structure across the seven shallow M. cavernosa sampling sites, the SNP analyses revealed significant pairwise population differentiation, suggesting that differentiation is greater between eastern and western sites. This study provides insight into methodological differences between microsatellite and SNP markers including potential trade-offs between marker-specific biases, sample size, sequencing costs, and the ability to resolve subtle patterns of population genetic structure. Furthermore, this study suggests that locations in western Cuba may play important roles in this species’ regional metapopulation dynamics and therefore may merit incorporation into developing international management efforts in addition to the local management the sites receive.
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Cerullo AR, Lai TY, Allam B, Baer A, Barnes WJP, Barrientos Z, Deheyn DD, Fudge DS, Gould J, Harrington MJ, Holford M, Hung CS, Jain G, Mayer G, Medina M, Monge-Nájera J, Napolitano T, Espinosa EP, Schmidt S, Thompson EM, Braunschweig AB. Comparative Animal Mucomics: Inspiration for Functional Materials from Ubiquitous and Understudied Biopolymers. ACS Biomater Sci Eng 2020; 6:5377-5398. [DOI: 10.1021/acsbiomaterials.0c00713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Antonio R. Cerullo
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Tsoi Ying Lai
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Alexander Baer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - W. Jon P. Barnes
- Centre for Cell Engineering, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Zaidett Barrientos
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Dimitri D. Deheyn
- Marine Biology Research Division-0202, Scripps Institute of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Douglas S. Fudge
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - John Gould
- School of Environmental and Life Sciences, University of Newcastle, University Drive, Callaghan, New South Wales 2308, Australia
| | - Matthew J. Harrington
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Mandë Holford
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- Department of Invertebrate Zoology, The American Museum of Natural History, New York, New York 10024, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The PhD Program in Biology, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Chia-Suei Hung
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Gaurav Jain
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, Pennsylvania 16802, United States
| | - Julian Monge-Nájera
- Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, Mercedes de Montes de Oca, San José 474-2050, Costa Rica
| | - Tanya Napolitano
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
| | - Emmanuelle Pales Espinosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, United States
| | - Stephan Schmidt
- Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Eric M. Thompson
- Sars Centre for Marine Molecular Biology, Thormøhlensgt. 55, 5020 Bergen, Norway
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | - Adam B. Braunschweig
- The PhD Program in Biochemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- The Advanced Science Research Center, Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, New York 10031, United States
- Department of Chemistry and Biochemistry, Hunter College, 695 Park Avenue, New York, New York 10065, United States
- The PhD Program in Chemistry, Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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Peled Y, Drake JL, Malik A, Almuly R, Lalzar M, Morgenstern D, Mass T. Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata. ACTA ACUST UNITED AC 2020; 2:8. [PMID: 32724895 PMCID: PMC7115838 DOI: 10.1186/s42833-020-00014-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins’ gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.
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Affiliation(s)
- Yanai Peled
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Jeana L Drake
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Assaf Malik
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Ricardo Almuly
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Core Unit, University of Haifa, Haifa, Israel
| | - David Morgenstern
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Mass
- Marine Biology Department, University of Haifa, Haifa, Israel
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Drake JL, Mass T, Stolarski J, Von Euw S, van de Schootbrugge B, Falkowski PG. How corals made rocks through the ages. GLOBAL CHANGE BIOLOGY 2020; 26:31-53. [PMID: 31696576 PMCID: PMC6942544 DOI: 10.1111/gcb.14912] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 05/03/2023]
Abstract
Hard, or stony, corals make rocks that can, on geological time scales, lead to the formation of massive reefs in shallow tropical and subtropical seas. In both historical and contemporary oceans, reef-building corals retain information about the marine environment in their skeletons, which is an organic-inorganic composite material. The elemental and isotopic composition of their skeletons is frequently used to reconstruct the environmental history of Earth's oceans over time, including temperature, pH, and salinity. Interpretation of this information requires knowledge of how the organisms formed their skeletons. The basic mechanism of formation of calcium carbonate skeleton in stony corals has been studied for decades. While some researchers consider coral skeletons as mainly passive recorders of ocean conditions, it has become increasingly clear that biological processes play key roles in the biomineralization mechanism. Understanding the role of the animal in living stony coral biomineralization and how it evolved has profound implications for interpreting environmental signatures in fossil corals to understand past ocean conditions. Here we review historical hypotheses and discuss the present understanding of how corals evolved and how their skeletons changed over geological time. We specifically explain how biological processes, particularly those occurring at the subcellular level, critically control the formation of calcium carbonate structures. We examine the different models that address the current debate including the tissue-skeleton interface, skeletal organic matrix, and biomineralization pathways. Finally, we consider how understanding the biological control of coral biomineralization is critical to informing future models of coral vulnerability to inevitable global change, particularly increasing ocean acidification.
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Affiliation(s)
- Jeana L Drake
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | | | - Stanislas Von Euw
- Trinity Centre for Bioengineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | | | - Paul G Falkowski
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ, USA
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Conci N, Wörheide G, Vargas S. New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes. Genome Biol Evol 2019; 11:3068-3081. [PMID: 31518412 PMCID: PMC6824150 DOI: 10.1093/gbe/evz199] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
A general trend observed in animal skeletomes-the proteins occluded in animal skeletons-is the copresence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend. However, distributions and phylogenetic analyses of biomineralization-related genes are often based on only a few species, with other anthozoan calcifiers such as octocorals (soft corals), not being fully considered. We de novo assembled the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeleton vs. calcitic sclerites) and data-mined published nonbilaterian transcriptome resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoral skeletome components. Cnidaria shared no skeletome proteins with Placozoa or Ctenophora, but did share some skeletome proteins with Porifera, such as galaxin-related proteins. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes such as secreted acidic proteins, scleritin, and carbonic anhydrases, and propose an early, single biomineralization-recruitment event for galaxin sensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion into the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e., aragonite/calcite) with no differences in the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points to skeletome homogeneity within but not between groups of calcifying cnidarians, although some proteins such as galaxins and SCRiP-3a could represent instances of commonality.
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Affiliation(s)
- Nicola Conci
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
- SNSB—Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
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Neder M, Laissue PP, Akiva A, Akkaynak D, Albéric M, Spaeker O, Politi Y, Pinkas I, Mass T. Mineral formation in the primary polyps of pocilloporoid corals. Acta Biomater 2019; 96:631-645. [PMID: 31302296 DOI: 10.1016/j.actbio.2019.07.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/18/2019] [Accepted: 07/09/2019] [Indexed: 02/07/2023]
Abstract
In reef-building corals, larval settlement and its rapid calcification provides a unique opportunity to study the bio-calcium carbonate formation mechanism involving skeleton morphological changes. Here we investigate the mineral formation of primary polyps, just after settlement, in two species of the pocilloporoid corals: Stylophora pistillata (Esper, 1797) and Pocillopora acuta (Lamarck, 1816). We show that the initial mineral phase is nascent Mg-Calcite, with rod-like morphology in P. acuta, and dumbbell morphology in S. pistillata. These structures constitute the first layer of the basal plate which is comparable to Rapid Accretion Deposits (Centers of Calcification, CoC) in adult coral skeleton. We found also that the rod-like/dumbbell Mg-Calcite structures in subsequent growth step will merge into larger aggregates by deposition of aragonite needles. Our results suggest that a biologically controlled mineralization of initial skeletal deposits occurs in three steps: first, vesicles filled with divalent ions are formed intracellularly. These vesicles are then transferred to the calcification site, forming nascent Mg-Calcite rod/pristine dumbbell structures. During the third step, aragonite crystals develop between these structures forming spherulite-like aggregates. STATEMENT OF SIGNIFICANCE: Coral settlement and recruitment periods are highly sensitive to environmental conditions. Successful mineralization during these periods is vital and influences the coral's chances of survival. Therefore, understanding the exact mechanism underlying carbonate precipitation is highly important. Here, we used in vivo microscopy, spectroscopy and molecular methods to provide new insights into mineral development. We show that the primary polyp's mineral arsenal consists of two types of minerals: Mg-Calcite and aragonite. In addition, we provide new insights into the ion pathway by showing that divalent ions are concentrated in intracellular vesicles and are eventually deposited at the calcification site.
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Affiliation(s)
- Maayan Neder
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Interuniversity Institute of Marine Sciences, Eilat 88103, Israel
| | | | - Anat Akiva
- Laboratory of Materials and Interface Chemistry and Center for Multiscale Electron Microscopy, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Derya Akkaynak
- The Interuniversity Institute of Marine Sciences, Eilat 88103, Israel; Department of Marine Technologies, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Marie Albéric
- Max-Planck Institute of Colloids and Interfaces, Potsdam-Golm 14476, Germany
| | - Oliver Spaeker
- Max-Planck Institute of Colloids and Interfaces, Potsdam-Golm 14476, Germany
| | - Yael Politi
- Max-Planck Institute of Colloids and Interfaces, Potsdam-Golm 14476, Germany
| | - Iddo Pinkas
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Tali Mass
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3498838, Israel.
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36
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Evans JS. The Biomineralization Proteome: Protein Complexity for a Complex Bioceramic Assembly Process. Proteomics 2019; 19:e1900036. [DOI: 10.1002/pmic.201900036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Indexed: 12/20/2022]
Affiliation(s)
- John Spencer Evans
- Laboratory for Chemical PhysicsDepartment of Skeletal and Craniofacial BiologyNew York University College of Dentistry New York NY 10010 USA
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37
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Yuyama I, Higuchi T. Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions. PeerJ 2019; 7:e7241. [PMID: 31341732 PMCID: PMC6637933 DOI: 10.7717/peerj.7241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/02/2019] [Indexed: 12/14/2022] Open
Abstract
Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO3.
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Affiliation(s)
- Ikuko Yuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tomihiko Higuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Zhao R, Takeuchi T, Luo YJ, Ishikawa A, Kobayashi T, Koyanagi R, Villar-Briones A, Yamada L, Sawada H, Iwanaga S, Nagai K, Satoh N, Endo K. Dual Gene Repertoires for Larval and Adult Shells Reveal Molecules Essential for Molluscan Shell Formation. Mol Biol Evol 2019; 35:2751-2761. [PMID: 30169718 PMCID: PMC6231486 DOI: 10.1093/molbev/msy172] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA-CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.
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Affiliation(s)
- Ran Zhao
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yi-Jyun Luo
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Akito Ishikawa
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tatsushi Kobayashi
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | | | - Kiyohito Nagai
- Pearl Research Institute, Mikimoto CO., LTD, Shima, Mie, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Yuan X, Huang H, Zhou W, Guo Y, Yuan T, Liu S. Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:151-160. [PMID: 30612219 DOI: 10.1007/s10126-018-9864-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Recent studies have indicated that various corals might have different degrees of resistance to elevated CO2 levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO2 levels. The calcification rates were higher in high CO2 treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca2+ transporters were present in the calcium signaling pathway, which could be important in the CO2 regulation of coral calcification. The gene expression levels of many CO2 and HCO3- transporters were not affected by elevated CO2. Nevertheless, high CO2 levels did have an effect on the expression of certain Ca2+ transporters. The upregulation of Ca2+ transporters likely explained the higher resistance of A. austera to high CO2 than A. cerealis.
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Affiliation(s)
- Xiangcheng Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Weihua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Yajuan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Equipment Public Service Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
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40
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Yuyama I, Higuchi T. Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions. PeerJ 2019. [PMID: 31341732 DOI: 10.7287/peerj.7241v0.1/reviews/2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO3.
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Affiliation(s)
- Ikuko Yuyama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tomihiko Higuchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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41
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Zhao R, Takeuchi T, Luo YJ, Ishikawa A, Kobayashi T, Koyanagi R, Villar-Briones A, Yamada L, Sawada H, Iwanaga S, Nagai K, Satoh N, Endo K. Dual Gene Repertoires for Larval and Adult Shells Reveal Molecules Essential for Molluscan Shell Formation. Mol Biol Evol 2018. [PMID: 30169718 DOI: 10.1093/molbev/msy1172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA-CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.
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Affiliation(s)
- Ran Zhao
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yi-Jyun Luo
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Akito Ishikawa
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tatsushi Kobayashi
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Alejandro Villar-Briones
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Japan
| | | | - Kiyohito Nagai
- Pearl Research Institute, Mikimoto CO., LTD, Shima, Mie, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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42
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Cunning R, Bay RA, Gillette P, Baker AC, Traylor-Knowles N. Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution. Sci Rep 2018; 8:16134. [PMID: 30382153 PMCID: PMC6208414 DOI: 10.1038/s41598-018-34459-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/19/2018] [Indexed: 12/22/2022] Open
Abstract
Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.
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Affiliation(s)
- R Cunning
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA. .,Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - R A Bay
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - P Gillette
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - A C Baker
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - N Traylor-Knowles
- Department of Marine Biology and Ecology, University of Miami Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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43
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Guzman C, Shinzato C, Lu TM, Conaco C. Transcriptome analysis of the reef-building octocoral, Heliopora coerulea. Sci Rep 2018; 8:8397. [PMID: 29849113 PMCID: PMC5976621 DOI: 10.1038/s41598-018-26718-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 05/09/2018] [Indexed: 01/15/2023] Open
Abstract
The blue coral, Heliopora coerulea, is a reef-building octocoral that prefers shallow water and exhibits optimal growth at a temperature close to that which causes bleaching in scleractinian corals. To better understand the molecular mechanisms underlying its biology and ecology, we generated a reference transcriptome for H. coerulea using next-generation sequencing. Metatranscriptome assembly yielded 90,817 sequences of which 71% (64,610) could be annotated by comparison to public databases. The assembly included transcript sequences from both the coral host and its symbionts, which are related to the thermotolerant C3-Gulf ITS2 type Symbiodinium. Analysis of the blue coral transcriptome revealed enrichment of genes involved in stress response, including heat-shock proteins and antioxidants, as well as genes participating in signal transduction and stimulus response. Furthermore, the blue coral possesses homologs of biomineralization genes found in other corals and may use a biomineralization strategy similar to that of scleractinians to build its massive aragonite skeleton. These findings thus offer insights into the ecology of H. coerulea and suggest gene networks that may govern its interactions with its environment.
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Affiliation(s)
- Christine Guzman
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines.,Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba, 277-8564, Japan
| | - Tsai-Ming Lu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Cecilia Conaco
- Marine Science Institute, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines.
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44
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Takeuchi T, Plasseraud L, Ziegler-Devin I, Brosse N, Shinzato C, Satoh N, Marin F. Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization. J Struct Biol 2018; 203:219-229. [PMID: 29859330 DOI: 10.1016/j.jsb.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 02/01/2023]
Abstract
To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysaccharides constitute the major component of the SOM, its contribution to coral skeleton formation is poorly understood. To this end, we analyzed the SOM of the massive colonial coral, Porites australiensis, the skeleton of which has drawn great research interest because it records environmental conditions throughout the life of the colony. The coral skeleton was extensively cleaned, decalcified with acetic acid, and organic fractions were separated based on solubility. These fractions were analyzed using various techniques, including SDS-PAGE, FT-IR, in vitro crystallization, CHNS analysis, chromatography analysis of monosaccharide and enzyme-linked lectin assay (ELLA). We confirmed the acidic nature of SOM and the presence of sulphate, which is thought to initiate CaCO3 crystallization. In order to analyze glycan structures, we performed ELLA on the soluble SOM for the first time and found that it exhibits strong specificity to Datura stramonium lectin (DSL). Furthermore, using biotinylated DSL with anti-biotin antibody conjugated to nanogold, in situ localization of DSL-binding polysaccharides in the P. australiensis skeleton was performed. Signals were distributed on the surfaces of fiber-like crystals of the skeleton, suggesting that polysaccharides may modulate crystal shape. Our study emphasizes the importance of sugar moieties in biomineralization of scleractinian corals.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | - Laurent Plasseraud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR CNRS 6302, Faculté des Sciences Mirande, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
| | - Isabelle Ziegler-Devin
- LERMAB, Faculté des Sciences & Technologies -Campus Aiguillettes, Université de Lorraine, Vandœuvre-Lès-Nancy, France
| | - Nicolas Brosse
- LERMAB, Faculté des Sciences & Technologies -Campus Aiguillettes, Université de Lorraine, Vandœuvre-Lès-Nancy, France
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Department of Marine Bioscience Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Frédéric Marin
- UMR CNRS 6282 Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne - Franche-Comté (UBFC), Dijon, France
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45
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Cheng H, Zhao H, Yang T, Ruan S, Wang H, Xiang N, Zhou H, Li QX, Diao X. Comparative evaluation of five protocols for protein extraction from stony corals (Scleractinia) for proteomics. Electrophoresis 2018; 39:1062-1070. [DOI: 10.1002/elps.201700436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/04/2018] [Accepted: 01/16/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Huamin Cheng
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Hongwei Zhao
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Tinghan Yang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Sunlan Ruan
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Haihua Wang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Nan Xiang
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Hailong Zhou
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Institute of Tropical Agriculture and Forestry; Hainan University; Haikou P. R. China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering; University of Hawaii at Manoa; Honolulu USA
| | - Xiaoping Diao
- State Key Laboratory of South China Sea Marine Resource Utilization; Hainan University; Haikou P. R. China
- Ministry of Eduction Key Laboratory of Tropical Island Ecology; Hainan Normal University; Haikou P. R. China
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46
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Mayfield AB, Chen YJ, Lu CY, Chen CS. The proteomic response of the reef coral Pocillopora acuta to experimentally elevated temperatures. PLoS One 2018; 13:e0192001. [PMID: 29385204 PMCID: PMC5792016 DOI: 10.1371/journal.pone.0192001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Although most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a nine-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially concentrated proteins (DCPs) were removed from the gels and sequenced with mass spectrometry. Sixty unique DCPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more responsive to high temperature at the protein-level than the coral hosts in which they resided at the two-week sampling time. Furthermore, proteins involved in the stress response were more likely to be documented at different cellular concentrations across temperature treatments in Symbiodinium, whereas the temperature-sensitive host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates have differing strategies for acclimating to elevated temperatures.
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Affiliation(s)
- Anderson B. Mayfield
- Khaled bin Sultan Living Oceans Foundation, Annapolis, MD, United States of America
- Taiwan Coral Research Center, Checheng, Pingtung, Taiwan
- * E-mail:
| | - Yi-Jyun Chen
- Taiwan Coral Research Center, Checheng, Pingtung, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Research Resources and Development, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chii-Shiarng Chen
- Taiwan Coral Research Center, Checheng, Pingtung, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung, Taiwan
- Graduate Institute of Marine Biotechnology, National Dong-Hwa University, Checheng, Pingtung, Taiwan
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47
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Mass T, Drake JL, Heddleston JM, Falkowski PG. Nanoscale Visualization of Biomineral Formation in Coral Proto-Polyps. Curr Biol 2017; 27:3191-3196.e3. [PMID: 29033329 DOI: 10.1016/j.cub.2017.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/11/2017] [Accepted: 09/06/2017] [Indexed: 11/16/2022]
Abstract
Calcium carbonate platforms produced by reef-building stony corals over geologic time are pervasive features around the world [1]; however, the mechanism by which these organisms produce the mineral is poorly understood (see review by [2]). It is generally assumed that stony corals precipitate calcium carbonate extracellularly as aragonite in a calcifying medium between the calicoblastic ectoderm and pre-existing skeleton, separated from the overlying seawater [2]. The calicoblastic ectoderm produces extracellular matrix (ECM) proteins, secreted to the calcifying medium [3-6], which appear to provide the nucleation, alteration, elongation, and inhibition mechanisms of the biomineral [7] and remain occluded and preserved in the skeleton [8-10]. Here we show in cell cultures of the stony coral Stylophora pistillata that calcium is concentrated in intracellular pockets that are subsequently exported from the cell where a nucleation process leads to the formation of extracellular aragonite crystals. Analysis of the growing crystals by lattice light-sheet microscopy suggests that the crystals elongate from the cells' surfaces outward.
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Affiliation(s)
- Tali Mass
- University of Haifa, Department of Marine Biology, The Leon H. Charney School of Marine Sciences, Multi Purpose Boulevard, Mt. Carmel, Haifa 3498838, Israel.
| | - Jeana L Drake
- Rutgers University, Department of Marine and Coastal Sciences, Dudley Road, New Brunswick, NJ 08901, USA
| | - John M Heddleston
- Howard Hughes Medical Institute Janelia Research Campus, Advanced Imaging Center, Helix Drive, Ashburn, VA 20147, USA
| | - Paul G Falkowski
- Rutgers University, Department of Marine and Coastal Sciences, Dudley Road, New Brunswick, NJ 08901, USA; Rutgers University, Department of Earth and Planetary Sciences, Taylor Road, Piscataway, NJ 08854, USA
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Flores RL, Livingston BT. The skeletal proteome of the sea star Patiria miniata and evolution of biomineralization in echinoderms. BMC Evol Biol 2017; 17:125. [PMID: 28583083 PMCID: PMC5460417 DOI: 10.1186/s12862-017-0978-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/23/2017] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Proteomic studies of skeletal proteins have revealed large, complex mixtures of proteins occluded within the mineral. Many skeletal proteomes contain rapidly evolving proteins with repetitive domains, further complicating our understanding. In echinoderms, proteomic analysis of the skeletal proteomes of mineralized tissues of the sea urchin Strongylocentrotus purpuratus prominently featured spicule matrix proteins with repetitive sequences linked to a C-type lectin domain. A comparative study of the brittle star Ophiocoma wendtii skeletal proteome revealed an order of magnitude fewer proteins containing C-type lectin domains. A number of other proteins conserved in the skeletons of the two groups were identified. Here we report the complete skeletal proteome of the sea star Patiria miniata and compare it to that of the other echinoderm groups. RESULTS We have identified eighty-five proteins in the P. miniata skeletal proteome. Forty-two percent of the proteins were determined to be homologous to proteins found in the S. purpuratus skeletal proteomes. An additional 34 % were from similar functional classes as proteins in the urchin proteomes. Thirteen percent of the P. miniata proteins had homologues in the O. wendtii skeletal proteome with an additional 29% showing similarity to brittle star skeletal proteins. The P. miniata skeletal proteome did not contain any proteins with C-lectin domains or with acidic repetitive regions similar to the sea urchin or brittle star spicule matrix proteins. MSP130 proteins were also not found. We did identify a number of proteins homologous between the three groups. Some of the highly conserved proteins found in echinoderm skeletons have also been identified in vertebrate skeletons. CONCLUSIONS The presence of proteins conserved in the skeleton in three different echinoderm groups indicates these proteins are important in skeleton formation. That a number of these proteins are involved in skeleton formation in vertebrates suggests a common origin for some of the fundamental processes co-opted for skeleton formation in deuterostomes. The proteins we identify suggest transport of proteins and calcium via endosomes was co-opted to this function in a convergent fashion. Our data also indicate that modifications to the process of skeleton formation can occur through independent co-option of proteins following species divergence as well as through domain shuffling.
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Affiliation(s)
- Rachel L. Flores
- Department of Biological Sciences, California State University, 1250 Bellflower Blvd, Long Beach, CA 90840 USA
| | - Brian T. Livingston
- Department of Biological Sciences, California State University, 1250 Bellflower Blvd, Long Beach, CA 90840 USA
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Ohno Y, Iguchi A, Shinzato C, Inoue M, Suzuki A, Sakai K, Nakamura T. An aposymbiotic primary coral polyp counteracts acidification by active pH regulation. Sci Rep 2017; 7:40324. [PMID: 28098180 PMCID: PMC5241827 DOI: 10.1038/srep40324] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/05/2016] [Indexed: 01/12/2023] Open
Abstract
Corals build their skeletons using extracellular calcifying fluid located in the tissue-skeleton interface. However, the mechanism by which corals control the transport of calcium and other ions from seawater and the mechanism of constant alkalization of calcifying fluid are largely unknown. To address these questions, we performed direct pH imaging at calcification sites (subcalicoblastic medium, SCM) to visualize active pH upregulation in live aposymbiotic primary coral polyps treated with HCl-acidified seawater. Active alkalization was observed in all individuals using vital staining method while the movement of HPTS and Alexa Fluor to SCM suggests that certain ions such as H+ could diffuse via a paracellular pathway to SCM. Among them, we discovered acid-induced oscillations in the pH of SCM (pHSCM), observed in 24% of polyps examined. In addition, we discovered acid-induced pH up-regulation waves in 21% of polyps examined, which propagated among SCMs after exposure to acidified seawater. Our results showed that corals can regulate pHSCM more dynamically than was previously believed. These observations will have important implications for determining how corals regulate pHSCM during calcification. We propose that corals can sense ambient seawater pH via their innate pH-sensitive systems and regulate pHSCM using several unknown pH-regulating ion transporters that coordinate with multicellular signaling occurring in coral tissue.
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Affiliation(s)
- Yoshikazu Ohno
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
| | - Akira Iguchi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago, Okinawa 905-2192, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Mayuri Inoue
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530, Japan
| | - Atsushi Suzuki
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Kazuhiko Sakai
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Takashi Nakamura
- Marine and Environmental Sciences Course, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
- Japan Science and Technology Agency (JST)/Japan International Cooperation Agency (JICA) SATREPS, Tokyo, Japan
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